WU-BLAST (Protein Databases)
Introduction
WU-BLAST stands for Washington University Basic Local Alignment Search Tool. The emphasis of this tool is to find regions of sequence similarity or homology quickly, with minimum loss of sensitivity. This will yield functional and evolutionary clues about the structure and function of your novel sequence. Dr Warren Gish at Washington University released this first "gapped" version of BLAST allowing for gapped alignments and statistics.
How to use this tool
Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.
Each tool has at least 2 steps, but most of them have more:
- The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
- In the following steps, the user has the possibility to change the default tool parameters
- And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server
Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.
Step 1 - Database
Databases
Database
| Database Name | Description | Abbreviation |
|---|---|---|
| UniProt Knowledgebase | The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-references. Search UniProtKB to retrieve "everything that is known" about a particular sequence | uniprotkb |
| UniProtKB/Swiss-Prot | The manually curated subsection of the UniProt Knowledgebase | uniprotkb_swissprot |
| UniProtKB/Swiss-Prot isoforms | The isoform sequences for the manually curated subsection of the UniProt Knowledgebase | uniprotkb_swissprotsv |
| UniProtKB/TrEMBL | Subsection of the UniProt Knowledgebase derived from EMBL-Bank coding sequence translations with annotation produced by an automated process. | uniprotkb_trembl |
| UniProtKB Taxonomic Subsets | ||
| UniProtKB Archaea | Taxonomic subset of the UniProt Knowledgebase for archaea | uniprotkb_archaea |
| UniProtKB Arthropoda | Taxonomic subset of the UniProt Knowledgebase for arthropoda | uniprotkb_arthropoda |
| UniProtKB Bacteria | Taxonomic subset of the UniProt Knowledgebase for bacteria | uniprotkb_bacteria |
| UniProtKB Complete Microbial Proteomes | Taxonomic subset of the UniProt Knowledgebase for complete microbial proteomes | uniprotkb_complete_microbial_proteomes |
| UniProtKB Eukaryota | Taxonomic subset of the UniProt Knowledgebase for eukaryota | uniprotkb_eukaryota |
| UniProtKB Fungi | Taxonomic subset of the UniProt Knowledgebase for fungi | uniprotkb_fungi |
| UniProtKB Human | Taxonomic subset of the UniProt Knowledgebase for human | uniprotkb_human |
| UniProtKB Mammals | Taxonomic subset of the UniProt Knowledgebase for mammals | uniprotkb_mammals |
| UniProtKB Nematoda | Taxonomic subset of the UniProt Knowledgebase for nematoda | uniprotkb_nematoda |
| UniProtKB PDB | Taxonomic subset of the UniProt Knowledgebase for PDB | uniprotkb_pdb |
| UniProtKB Rodents | Taxonomic subset of the UniProt Knowledgebase for rodents | uniprotkb_rodents |
| UniProtKB Vertebrates | Taxonomic subset of the UniProt Knowledgebase for vertebrates | uniprotkb_vertebrates |
| UniProtKB Viridiplantae | Taxonomic subset of the UniProt Knowledgebase for viridiplantae | uniprotkb_viridiplantae |
| UniProtKB Viruses | Taxonomic subset of the UniProt Knowledgebase for viruses | uniprotkb_viruses |
| UniProt Clusters | The UniProt Reference Clusters (UniRef) databases combine closely related sequences into a single record to speed up searches. | |
| UniProt Clusters 100% | The UniProt Reference Clusters (UniRef) containing sequences which are 100% identical. | uniref100 |
| UniProt Clusters 100% (SEG filtered) | UniProt Reference Clusters database (SEG filtered) with entries that have 100% mutual sequence identity. | uniref100_seg |
| UniProt Clusters 90% | The UniProt Reference Clusters (UniRef) containing sequences which are 90% identical. | uniref90 |
| UniProt Clusters 50% | The UniProt Reference Clusters (UniRef) containing sequences which are 50% identical. | uniref50 |
| Patents | ||
| EPO Patent Protein Sequences | Protein sequences appearing in patents from the European Patent Office (EPO) | epop |
| JPO Patent Protein Sequences | Protein sequences appearing in patents from the Japanese Patent Office (JPO) | jpop |
| KIPO Patent Protein Sequences | Protein sequences appearing in patents from the Korean Intelectual Property Office (KIP0). | kpop |
| USPTO Patent Protein Sequences | Protein sequences appearing in patents from the United States Patent and Trademark Office (USPTO) | uspop |
| NR Patent Proteins Level-1 | Non-redundant Patent Protein sequences Level 1 covering data from the EPO, JPO, KIPO and USPTO | nrpl1 |
| NR Patent Proteins Level-2 | Non-redundant Patent Protein sequences Level 2 covering data from the EPO, JPO, KIPO and USPTO | nrpl2 |
| Structure | ||
| Protein Structure Sequences | Protein sequences from structures described in the Brookhaven Protein Data Bank (PDB) | pdb |
| Structural Genomics Targets | Structural Genomic Targets (SGT) database | sgt |
| Other Protein Databases | ||
| UniProt Archive | The UniProt Archive (UniParc) contains available protein sequences collected from many different sources. The sequence data are archived to facilitate examination of changes to sequence data. Search UniParc if you want to examine the "history" of a particular sequence. | uniparc |
| IntAct | The IntAct sequence database is derived from UniProt entries and data from MassSpec experiments submitted to the IntAct protein-interaction database. | intact |
| IMGT/HLA | The human major histocompatibility complex (HLA) section of the the international immunogenetics (IMGT) database. | imgthlap |
| IPD-KIR | Human Killer-cell Immunoglobulin-like Receptors (KIR) sequence in the Immuno Polymorphism Database (IPD) | ipdkirp |
| IPD-MHC | Major Histocompatibility Complex (MHC) section of the Immuno Polymorphism Database (IPD) | ipdmhcp |
Default value is: UniProt Knowledgebase [uniprotkb]
Step 2 - Sequence
Sequence Input Window
The query sequence can be entered directly into this form. The sequence can be be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is a limit of 1MB for the sequence entry.
Sequence File Upload
A file containing a valid sequence in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) can be used as input for the sequence similarity search. Word processor files may yield unpredictable results as hidden/control characters may be present. It is best to save files with the Unix format option to avoid hidden Windows characters. There is a limit of 1MB for the sequence entry.
Sequence Type
Indicates if the sequence is protein or DNA/RNA.
| Type | Abbreviation |
|---|---|
| PROTEIN | protein |
| DNA/RNA | dna |
Default value is: PROTEIN [protein]
Step 3 - Parameters
Program
The BLAST program to be used for the Sequence Similarity Search.
| Program Name | Description | Abbreviation |
|---|---|---|
| blastp | Compares an amino acid query sequence against a protein sequence database | blastp |
| blastx | Compares a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames | blastx |
Default value is: blastp
Matrix
The comparison matrix to be used to score alignments when searching the database
| Matrix Name | Abbreviation |
|---|---|
| BLOSUM62 | blosum62 |
| BLOSUM30 | blosum30 |
| BLOSUM35 | blosum35 |
| BLOSUM40 | blosum40 |
| BLOSUM45 | blosum45 |
| BLOSUM50 | blosum50 |
| BLOSUM65 | blosum65 |
| BLOSUM70 | blosum70 |
| BLOSUM75 | blosum75 |
| BLOSUM80 | blosum80 |
| BLOSUM85 | blosum85 |
| BLOSUM90 | blosum90 |
| BLOSUM100 | blosum100 |
| Gonnet | GONNET |
| PAM10 | pam10 |
| PAM20 | pam20 |
| PAM30 | pam30 |
| PAM40 | pam40 |
| PAM50 | pam50 |
| PAM60 | pam60 |
| PAM70 | pam70 |
| PAM80 | pam80 |
| PAM90 | pam90 |
| PAM100 | pam100 |
| PAM110 | pam110 |
| PAM120 | pam120 |
| PAM130 | pam130 |
| PAM140 | pam140 |
| PAM150 | pam150 |
| PAM160 | pam160 |
| PAM170 | pam170 |
| PAM180 | pam180 |
| PAM190 | pam190 |
| PAM200 | pam200 |
| PAM210 | pam210 |
| PAM220 | pam220 |
| PAM230 | pam230 |
| PAM240 | pam240 |
| PAM250 | pam250 |
| PAM260 | pam260 |
| PAM270 | pam270 |
| PAM280 | pam280 |
| PAM290 | pam290 |
| PAM300 | pam300 |
| PAM310 | pam310 |
| PAM320 | pam320 |
| PAM330 | pam330 |
| PAM340 | pam340 |
| PAM350 | pam350 |
| PAM360 | pam360 |
| PAM370 | pam370 |
| PAM380 | pam380 |
| PAM390 | pam390 |
| PAM400 | pam400 |
| PAM410 | pam410 |
| PAM420 | pam420 |
| PAM430 | pam430 |
| PAM440 | pam440 |
| PAM450 | pam450 |
| PAM460 | pam460 |
| PAM470 | pam470 |
| PAM480 | pam480 |
| PAM490 | pam490 |
| PAM500 | pam500 |
Default value is: BLOSUM62 [blosum62]
- Additional information
Expectation Threshold
Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance.
Default value is: 10 (default) [10]
Filter
Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather than meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.
| Name | Desciption | Value |
|---|---|---|
| none | No filtering of the query sequence. | none |
| seg | Uses the seg filter to replace low-complexity regions with 'X' in protein query sequences. | seg |
| xnu | Uses the xnu filter to mask statistically significant tandem repeats in protein query sequences. | xnu |
| seg+xnu | Uses both seg and xnu to filter low-complexity regions and statistically significant tandem repeats in protein query sequences. | seg+xnu |
Default value is: seg
View Filter
When set to "yes" the query sequence used for the search, post filtering, is shown in the output file.
Default value is: no [false]
Sensitivity
Increasing the sensitivity will increase the length of the search (longer execution times + more memory required), but increase the specificity of the results. A decrease will significantly speed up the search but decrease the sensitivity of the results.
| Sensitivity | Actual Setting | Value |
|---|---|---|
| very low | blastx/blastp: "W=5 T=1000 wink=2 hitdist=30"; blastn: "W=14 M=1 N=-3 Q=3 R=3 wink=2 hitdist=30"; tblastn/tblastx: "W=14 Q=3 R=3 wink=2 hitdist=30" | vlow |
| low | blastx/blastp: "T=1000 hitdist=40"; blastn: "W=12 M=1 N=-3 Q=3 R=3 hitdist=40"; tblastn/tblastx: "W=12 Q=3 R=3 hitdist=40" | low |
| medium | blastx/blastp: "hitdist=40"; blastn: "M=1 N=-3 Q=3 R=3"; tblastn/tblastx: "Q=3 R=3" | medium |
| normal | N/A | normal |
| high | blastx/blastp: "hspmax=0"; blastn: "W=9 gapW=24 hspmax=0"; tblastn/tblastx: "W=9 gapW=24 hspmax=0" | high |
Default value is: normal
Strand
For nucleotide sequences specify the sequence strand to be used for the search. By default both upper (provided) and lower (reverse complement of provided) strands are used, for single stranded sequences searching with only the upper or lower strand may provide better results.
Default value is: none
Scores
Maximum number of match score summaries reported in the result output.
Default value is: 50 (default) [50]
Alignments
Maximum number of match alignments reported in the result output.
Default value is: 50 (default) [50]
Sort
Sorts the scores in the score list of the output file.
Default value is: pvalue
Stats
The statistical model to use for assessing the significance of the hits found
Default value is: sump
topcomboN
Topcombo processing causes consistent sets of HSPs to be reported, such that any given HSP is allowed to be a member of just one set. Often, one wishes to see just the best set of consistent HSPs without any other "contaminants" in the output. This would be topcomboN=1.
Default value is: 1
Alignment Views
Formating for the alignments
| Name | Description | Value |
|---|---|---|
| pairwise | The query and match are output as a pairwsie alignment with a consensus line between the two sequences. In the consensus the match states are represented as: identical match as the base/residue, similarity as a '+' and missmatch as a space. | 1 |
| BLASTXML | Output NCBI BLAST XML instead of a plain text report. | 7 |
Default value is: pairwise [1]
Translation Table
Query Genetic code to use in translation
| Name | Value |
|---|---|
| N/A | -1 |
| Standard | 1 |
| Vertebrate Mitochondrial | 2 |
| Yeast Mitochondrial | 3 |
| Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma | 4 |
| Invertebrate Mitochondrial | 5 |
| Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear | 6 |
| Echinoderm Mitochondrial | 9 |
| Euplotid Nuclear | 10 |
| Bacterial and Plant Plastid | 11 |
| Alternative Yeast Nuclear | 12 |
| Ascidian Mitochondrial | 13 |
| Flatworm Mitochondrial | 14 |
| Blepharisma Macronuclear | 15 |
| Chlorophycean Mitochondrial | 16 |
| Trematode Mitochondrial | 21 |
| Scenedesmus obliquus mitochondrial | 22 |
| Thraustochytrium mitochondrial | 23 |
| Codon2004 | 1001 |
Default value is: Standard [1]
Step 4 - Submission
Job title
It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.
Email Notification
Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.
Email Address
If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).